Table 1. Comparison of four pan-genome methods on a test set of 11 Streptococcus pyogenes genomes.

	LS-BSR	GET_HOMOLOGUES	PGAP	ITEP
Clusters orthologs?	Yes	Yes	Yes	Yes
Open source?	Yes	Yes	Yes	Yes
Pan-genome calculation?	Yes	Yes	Yes	Yes
Lineage specific gene identification?	Yes	Yes	Yes	Yes
Functional annotation?	No	Yes	Yes	Yes
Analyzes user-defined genes?	Yes	No	No	Yes
Input files	“.fasta”	GenBank or “.faa”	“.faa”, “.fna”, “.ppt”	GenBank
Supported platforms	linux, OSX	linux/OSX	linux	linux/OSX
Core genome size	1318, 1350, 1426a	1232, 1234b	1332, 1366c,d	1342
Time (2 cores), only runtime	5 m 59 s, 1 m 53 s, 1 m 17 sa	25 m 14 s	29 m 59 s,199 m 58 sc,d	24 m 22 s

Notes.

^aTBLASTN, BLASTN, BLAT.

^bCOG, MCL.

^cMP, GF.

^dTaken from publication.